hlaHaplo2Geno: Get a genotype object from a specified haplotype object

In HIBAG: HIBAG -- HLA Genotype Imputation with Attribute Bagging

Description

To get a genotype object from a specified haplotype object by combining SNP alleles.

Usage

hlaHaplo2Geno(hapobj)

Arguments

hapobj

a haplotype object of hlaSNPHaploClass

Details

hapobj$haplotype is a numeric matrix, with an entry value 0 standing for B (ZERO A allele), 1 for A (ONE A allele) and others for missing values (missing SNP alleles are usually set to be NA).

Value

Return a hlaSNPHaploClass object, and it is a list:

haplotype	a haplotype matrix, “# of SNPs” - by - “2 x # of individuals”
sample.id	a vector of sample IDs
snp.id	a vector of SNP IDs
snp.position	a vector of SNP positions in basepair
snp.allele	a vector of characters with the format of “A allele/B allele”

Author(s)

Xiuwen Zheng

See Also

hlaMakeSNPGeno, hlaMakeSNPHaplo, hlaGenoSubset, hlaHaploSubset

HIBAG documentation built on May 2, 2019, 4:50 p.m.